Category: Weekly Posts

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Week 3

A response to the Lynch reading for Tuesday.

I’ve read the first couple sections, and the section on complexity and nonadaptive processes on page 8600, like Yana suggested. I haven’t read the rest of it.

My first impression was a bit of a “well, of course” situation. It makes perfect sense to me that not all changes are adaptive. It certainly sounds like complexity and directional evolution are contentious within the realm of biologists, which is good to be reminded of.

I found the examples of some species becoming ‘simpler’ really interesting. My first reaction was that of “How do we define ‘simple’ and ‘complex’?” It seemed like the argument in the paper was that of species becoming simpler over time showing that complex isn’t allways better. The examples being salamanders losing their legs and vent-worms going from having two opening to having one. These examples seem to be an assumption along the lines of the ‘if it looks like us it is complex’ complex. What if surviving with no legs or no mouth (in the cases of salamanders and vent-worms respectively) is ‘more complex’ somehow. For example, one might need a bi-directional digestive tract to deal with having just one opening, which takes a very complicated gut to deal with things. I can’t say if this is the case or not, but I am uncomfortable accepting the assumption that X change is a ‘simplification’.

Another question I have is based on the following statement:

“However, the effects of mutation and recombination are nonrandom, and by magnifying the role of chance, genetic drift indirectly imposes directionality ….”

Would someone be able to explain how mutation and recombination are nonrandom? I thought that they were by definition random events that were then selected for/against/neutral.

One last thing I’d like to propose is that maybe a better explanation for the survival/fitness of complex organisms can come from their relatively long life instead of them being better replicatiors? If complex multicellular organisms are not as good at replicating, maybe they just hang around because they take longer to be killed off?

-Scott

A response to the Lynch reading for Tuesday.
I’ve read the first couple sections, and the section on complexity and nonadaptive processes on page 8600, like Yana suggested. I haven’t read the rest of it.
My first impression was a bit of a “well, of course” situation. It makes perfect sense to me that not all changes are adaptive. It certainly sounds like complexity and directional evolution are contentious within the realm of biologists, which is good to be reminded of.
I found the examples of some species becoming ‘simpler’ really interesting. My first reaction was that of “How do we define ‘simple’ and ‘complex’?” It seemed like the argument in the paper was that of species becoming simpler over time showing that complex isn’t allways better. The examples being salamanders losing their legs and vent-worms going from having two opening to having one. These examples seem to be an assumption along the lines of the ‘if it looks like us it is complex’ complex. What if surviving with no legs or no mouth (in the cases of salamanders and vent-worms respectively) is ‘more complex’ somehow. For example, one might need a bi-directional digestive tract to deal with having just one opening, which takes a very complicated gut to deal with things. I can’t say if this is the case or not, but I am uncomfortable accepting the assumption that X change is a ‘simplification’.
Another question I have is based on the following statement:
“However, the effects of mutation and recombination are nonrandom, and by magnifying the role of chance, genetic drift indirectly imposes directionality ….”
Would someone be able to explain how mutation and recombination are nonrandom? I thought that they were by definition random events that were then selected for/against/neutral.
One last thing I’d like to propose is that maybe a better explanation for the survival/fitness of complex organisms can come from their relatively long life instead of them being better replicatiors? If complex multicellular organisms are not as good at replicating, maybe they just hang around because they t
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Weekly Posts

Here’s my random thought for the week:

So, since I wasn’t able to explain it really well on Thursday, here’s my musing on how it might actually be good for your genes to kill yourself. So as Yana (I think?) was saying, if you’re past the point where you can reproduce, and you’re taking resources away from your children and not contributing much back, the best option is to go off yourself to increase your children’s, little bundles of genes that they are, chance of survival. Now, say that you’re young and fit and in your 20’s, but you’re also a total loser. People of the opposite gender hate you, you’re not particularly good at hunting and gathering and thus mostly rely on other people to get you fed, and your chances of being able to raise a family are pretty slim. Now suppose you have a brother. Your brother is slick and hot and awesome. He already has 15 kids running around, which carry roughly a quarter of your genes. You on the other hand will probably never have kids, and are a drain on your family, decreasing your brother’s kid’s chances of survival. Probably better if you kick it for their sakes then.

Course, at what point you can say that your case is hopeless and other people are better off without you strikes me as very difficult to determine, especially since as social creatures we could in the above situation help out our brother’s kid’s by getting food/fighting off beats/ etc. Also, plenty of people who already have kids/ SOs/ contribute of their family’s survival, etc. commit suicide as well, so I’m not saying this is some sort of adaptive explanation for suicide, I’m just thinking out a case where it could be better for your genes for you to kill yourself, even if you’re still of reproductive age.

As for the Lynch paper, I’m about halfway through it, and am finding it veeery interesting, though as Scott points out, I’m not aware of any sort of objective measurement for complexity (though I think we can safely objectively state that say, the tobacco mosaic virus is less complex than a pony). Cells by themselves are incredibly complex (note: all I know about cells I know from Biol200), so how much more complex, in the scheme of things, are eukaryotes and multicellular creatures? Also, why does this paper mention intelligent design every other page?

Finally, as an example of ‘things that look uber-complex but probably aren’t’ and some unicellular complexity, here’s a podcast I was listening to today about slime mold: http://www.cbc.ca/quirks/archives/09-10/qq-2010-01-23.html (scroll down to Taking Directions from Slime Mould, it also links to the original Science paper among a bunch of other things).

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Week 2

Of language acquisition, phylogeny and development

First off, a brief summary of week 2:

– Greg Bole gave us a great introduction to evolutionary biology focusing on replicators,defining the latter as a ‘stable pattern that can replicate itself’ (well-said, I think!); this opens up a wide territory for exploring what constitutes a replicator and how it applies outside biology.

– We also discussed levels of selection, more or less agreeing that the basic level of explanation should be on the gene (or, to generalise, replicator?) level; a higher level of organisation can be evoked in cases where gene-centred explanations fail (need specific examples; group selection to be discussed in more detail later)

– Fundamentals of biological evolution (molecular, and a touch of population genetics) were discussed very briefly, to give an idea of how evolution actually physically works in biology. Molecular (incl neutral) evolution will be covered in greater detail later; speciation and some population biology should be discussed tomorrow; but it would be nice to learn a little more about the mechanics of selection (population genetics stuff, etc), as I, for one, am absolutely clueless in that field*.

* This may be hard to believe, but there was for a long time (and still lingers) this divide between botanists and zoologists. This divide did not just happen on a taxonomic level — the approaches to evolutionary biology were fundamentally different in the two disciplines! Zoologists tend to focus more on speciation, selection, etc; ie. the actual mechanisms of how species diverge with a very population-based approach. Botanists, on the other hand, are obsessed with phylogenies and have a greater inclination to play with molecular evolution. It’s quite hilarious how the disciplines are all influenced tremendously by their histories, and this does have an impact on how we view and understand certain subjects!

This week, we should get a thorough grasp on phylogenies, focusing on how to read them correctly, but also something about how they’re made and what they actually mean. Some vile misconceptions (eg. the wretched progressive ‘ladder’ view of evolution) shall be ruthlessly despensed with. On Thursday, we should discuss the psychology paper, and spend the remaining time brainstorming some project ideas for the proposal due next week. (I’m as worried as you guys are, despite having known about this months ago…! Still have no idea/too many ideas for a topic…both simultaneously, somehow…)

And now, a response to Scott’s post on language and phylogenies: (too long to post as a comment…)

For one thing, phylogenies actually originated in linguistics. But perhaps what you mean is, do all languages fit on a single nice phylogeny? It’s interesting that you bring up creoles and pidgins — I find that example simply fascinating, and almost took language acquisition (LING452 methinks), except that it would’ve been a bit much that term. I guess a biological analogue to language learning/acquisition could be embryonic development:

It may help to think of languages as mature organisms, including genetics, epigenetics and various stuff that happened to them during their own lifetime. Some of that stuff is clearly inherited, some is murky, some has little influence on the progeny (among animals the example would be losing a limb). So, by analogy, one’s personal language* would also have some traits that are heritable, and some that are not. The language is still recogniseable as a ‘species’, if you will, but has some idiosyncratic streaks to it.

*One unfortunate thing is that Chomsky, who pretty much ruled the field of linguistics for decades, didn’t care much for individual variation within a language, and focused on the ‘pure’ language (or dialect) itself. Some linguists today are beginning to realise that was not such a good idea…

Now, in the case of pidgins and creoles, a pidgin would be sort of like mashing various parts of mature biological organisms together. This is seldom possible in the biological world, not spontaneously anyway. I say ‘seldom’ because things like grafting of both plants and some single cell organisms can generate these weird chimaeric hybrids. In the case of single celled organisms, this could actually be somewhat heritable, via cellular inheritance. But that’s murky ground. So biological ‘pidgins’ could be possible.

Creoles, on the other hand, are like mashing various parts of a mature biological organism together AND creating a whole new stable lineage that way. The gut reaction would be to call that ridiculous, but…luckily for us, biology is about as messy as linguistics, if not more so. Endosymbiosis is one complication where you actually get gene transfer between genomes, and the chimaeric organisms persist (there’s some stunningly complex stories out there, such as an organism with 6 different extant genome compartments (nuclei, plastids, mitochondria); in land plants we have cases of hybridisation between closely related species. The endosymbiosis case may be somewhat VERY LOOSELY analogous to creolisation, as we have multiple unrelated genomes and cells working in a single compartment, forming a single organism. It may be a stretch though.

Next up: what is an organism? =D

By the way, in April, Ford Doolittle (Dalhousie)  is giving a talk at the biodiversity research seminar (about constructive neutral evolution AFAIK); he’s a major MAJOR oponent of the bacterial tree; that is, he argues that because of all the lateral gene transfer (ie, between lineages rather than down along them), the tree concept fails for bacteria. It’s a long raging war, and if you guys are interested we could explore it. But in any case, closer to the day (it’s end of April, if I recall) I can remind you guys again, and highly recommend his talk. Afterwards, if there’s time, perhaps you could even pester him about LGT and the tree of life stuff.

Sorry for the really long post…

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Week 2 Weekly Posts

Okay, here’s my contribution to the week. We spoke a bit about levels of selection, so I thought I’d throw up a paper that shows where an individual’s interest is counter to a group’s interest. There’s also a bit about sex in there, which might be useful to start thinking about now. The paper is How to go extinct by mating too much: population consequences of male mate choice and efficiency n a sexual-asexual species complex by Katja U. Heubel, Daniel J. Rankin and Hanna Kokko.  2009.

First a bit of background, there’s this guppy-like fish genus called Poecilia. In several of the species in that genus, when they interbreed their offspring are these things called gynogens. They’re always female, and their offspring are clones. But while each egg they produce contains all the genetic material their offspring need, they still need to have the egg come into contact with sperm from one of the parental species to jump start the egg’s development. So, the gynogen species need to live around parental species to get the sperm off the males. Males theoretically get no benefit from fertilizing one of these eggs, since their genetic material isn’t passed on in the offspring (though one study found that females of the male’s species are more likely to mate with him if they see him having sex with one of gynogens. This puzzles everyone). This makes gynogens effectively sperm parasitizers.

What’s the problem here? Well the asexual fish should be able to produce twice the number of offspring as the sexual fish, since asexuals only need one individual of their own species to produce another, and sexual species need two individuals (this is officially called the ‘two fold cost of sex’). Thus, the gynogens should increase their population size much faster than the sexual species living in the same area, and should end up out-competing the sexual species for males by sheer numbers.  This causes the sexual species to go extinct, and then the asexual species soon follows because it no longer has any males to get sperm off of.

Two possible factors might throw this off: If males produce enough sperm, they should be able to fertilize all the females, sexual and asexual, and both lineages should persist. Or, males  might preferentially mate with their own species. These traits aren’t necessarily good for an individual to evolve though – sperm is costly to produce, and if the male is too discriminating, it might accidently pass up a chance to mate with a female of its own species, or waste too much time trying to tell whether a potential mate is a gynogen or not (these fish look very similar). The paper looked at these two traits, and constructed a model to see what levels of these traits would be best for the population as a whole (in other words, what amounts of male discrimination and sperm production combined lead to the long-term survival of the species?). They then compared the expected rates to rates in the wild.

I’ll spare the math because well, it’s mathy, and I’ve written a novel already. But, they found that their predicted numbers, and numbers observed in most gynogen populations didn’t match up. They pointed out that local populations have been observed to go extinct, and also that these fish are good colonizers, so as long as the extinction rate is low, individuals might ‘escape’ by colonizing a new area, and the whole game would play out over again. There’s quite a few other factors to consider with these fish (one being that the asexual species don’t completely overlap in niche with the sexual species, which would lessen a lot of competition), but I thought this example was interesting because it talked about group selection, and because gynogens are friggin weird and awesome.

For further reading about asexual fish (and uh, other vertebrates) I suggest Clonality by John Avise. It’s in Woodward. 🙂

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language Week 2

Re: Scott’s post about linguistic phylogeny

I tried to simply reply to the post itself, but I encountered the same “you must be logged in” glitch as previously complained about. What’s mysterious is that for some posts I am logged in, and for others I am not.

In any case, I think that a human population’s capacity to create a new grammar when one is lacking or unavailable does not exclude language from an evolutionary model. Specifically, I am thinking of the way that linguistic information is inherited from previous generations with astounding fidelity. And then mistakes are made in the copying process or populations migrate or whatever and the next thing you know, you have a dialect, then a new language altogether. This looks an awful lot like speciation to me.

It’s also important to remember that although an analogy may not fit to the letter, that doesn’t mean it isn’t still useful. While it would be brilliant if language evolved in literally the same way as genetic material, that would also be way too simple and make our lives far too easy. If you accept such a model as analogous and account for discrepancies therein, you can discover more about both subjects through their differences, and perhaps modify your understanding of them (hopefully in a useful way).

Switching gears completely, the Maddison reading for tomorrow made me wonder what speciation looks like. Is there a concrete example of this that has been observed? At what point do species split–that is, when can we start naming them in Latin? Can they only split in two directions, or can they branch off in three directions at once?

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Extra readings language Week 2 Weekly Posts

Universal Grammar and Linguistic Evolution

Okay, first off. I don’t know how familiar people are with the concept of Universal Grammar, but I’ll try to boil it down and give you a straightforward version. UG is composed of all things that are common to all human languages. This is not confined to spoken languages (ie, it includes sign language, which interestingly does seem to share many features with spoken language) but makes no attempts to explain orthography.

Now, here’s my point. If we’ve got UG, and we assume that there are certain features shared between languages that are selected for depending on the environment and the sociopolitical landscape (as some linguists have done, notably Oudeyer and Kaplan), UG probably won’t consist of a series of features, per se, since (by definition) those features will vary depending on where you are in the world. To assume otherwise would be rather like assuming that all organisms must consist of certain genes in order to be organisms.

What UG would consist of is rather what all those various linguistic features have in common, not just those things shared by successful features. If the linguistic features are genes, UG would therefore be analogous to the base pairs that compose all DNA.

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Week 2

Week 2 in review

Hmmm. I feel like I probably don’t have a great deal to contribute in the way of thinky things on the stuff we talked about this week, because as a Biology major, most of what was presented wasn’t new material for me. I found the Dawkins chapter interesting, though – I haven’t read The Selfish Gene (though I’ve heard good things and keep meaning to read it), but the process he goes through in generalizing evolution reminds me a great deal of mathmatics – you can work through a few examples of a given problem type (say, a linear regression), and in doing so generate a simplified formula that applies to all cases of the problem. Dawkins’ replicators are almost equivalent to the variable in a given formula – for evolution, the process holds true no matter what the variable is.

I also apologize for my somewhat flailing attempts at explaining population genetics/drift – I’m not much of a lecturer, although if anyone wants clarification some of that, I can do my best.

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language Week 2

Can linguistic phylogenies exist?

Is a historic (phylogenetic) tree a fair representation of the history of languages?

In a recent linguistics tutorial, we were talking about the formation of Pidgins and Creoles, languages that develop where different languages are forced to interact. The TA used a stereotypical story to try and illustrate how these languages develop, and I’ll recount it now as it helps to explain things.

++The story of Pidgins and Creoles++

Imagine an island where well to-do foreigners show up, set up banana plantations, and get the native locals to pick bananas for them. Neither people speaks the others’ language, and neither is particularly interested in learning the others’ language. The adults just want to conduct buisness as quickly as possible, and so develop a basic code for communicating.

The ‘Language’ that develops generally has little to no grammar. The words are usually taken from one language and then strung together in an arbitrary fashion. For example: “Three bushel banana, ten dollar.” Indicating a willingness to pay ten dollars for three bushels. The important thing here is that this is just a series of important words without grammar, they generally don’t get pluralized or otherwise modified. This is a Pidgin.

Later, the children born into this environment are brought up with most of the communication going on around them in this pidgin. Which means that they aren’t exposed to any grammar. The amazing thing is that without any exposure to a developed grammar they still create one of their own, using the words available but creating grammatical structures from scratch. This has been used as very strong evidence of the fact that every new generation has the potential to create a new language if there isn’t available data.

++Connected to what we’re talking about++

So what if languages are created from scratch? The concern discussed though was that, if languages are created from scratch each generation, how can we say that one language has decended directly from another? One can certainly claim that the majority of a language is similar to another one, but it seems like it would be more accurate to say that language X is 80% language Y, and 20% languages W and Z.

Unfortunately for anyone looking for parallels between linguistic and genetic evolution, this doesn’t seem like genetic evolution. Genetic evolution has a bunch of information passed from one individual to it’s offspring. Language is grown based on the available data, each generation.

So is this just a superficial difference? or perhaps it’s worth keeping in mind? I’ll try to remember to bring this up when we get around to linguistic evolution, and I’ll see if more information comes up in linguistics.

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Week 2

Topic Call for Papers

If there’s anything that’s been on my mind lately, it’s brainstorming ideas for the research proposal which will lead to a MURC talk and published paper; it would be really embarrassing to miss the deadline or bullshit through the presentation. It’s what this seminar/course centers around, after all, besides our wonderful guest lectures and learning about evolution before applying it anywhere.

I hope this qualifies for our agreed weekly blog posts, as I’m terribly bad with coming up with questions about what I don’t know or would like to expand on until I actually try to do something with the information I have and come across a dead end.

I can, however, come up with questions that can’t really be answered with any precision such as why are there Vampire bats, mockingbirds and finches? What other species shares this trait/niche? (Greg, that’s your fault.)

Anyway.

My primary area of interest concerns the evolution of imagination and fiction, from a biological-psychological perspective, I suppose. It’s a fairly broad topic, and I’m at a loss of how to go about it. I’ve been trying to get my hands on Brian Boyd’s “On the Origin of Stories: Evolution, Cognition, and Fiction,” but someone’s taken it out of the library, which has a new layout I can’t seem to navigate (Can someone tell me how to CWL login to that page? I can’t find the link!), and it isn’t available in any Chapters store (though I think it can be ordered online, which would take money and time). If anyone has articles to suggest, you can throw them at me.

Other interests concern the evolution of meditative practices, or the evolutionary biology-psychology of it, and the evolution of sex, but I’ll wait until Rosie Redfield’s talk to think about that. I’m also interested in the evolution of religious institutions as they “adapt” to new peoples and places. Or perhaps I’m not so much interested in religious institutions as I am in the universal cognitive mental modules that all relgious ideas share in common (are there some? I’m not talking about belief as much as how it is embodied in practice). What is the most stable type of practice among the most “successful” major relgions of today, and why? There seems to be a common need for relgious schooling for youth, prayer/chanting/singing that generates merit of some kind, confession of some kind, and being able to transfer merit to others, especially in service to the dead in afterlife/reinarnation, but also to the poor and needy.

What is everyone else interested in examining?

On the origin of stories: evolution, cognition, and fiction

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Week 1 - testing

Having problems with reply

I’m getting a little frustrated.  I see something I want to reply to and get the message “You must be logged in to leave a reply”

So I log in.  It takes me back to the main page (or worse, sometimes it takes me back to the UBC Blogs main page and I have to find my way back to this blog)

So I click on the post I want to reply to and get the message “You must be logged in to leave a reply”

You can see where this is going.   I feel like I’m in an endless loop.  Obviously I’m logged in, or I couldn’t post this rant.

So why can’t I reply to other posts?

Thanks for any help or suggestions.

EDIT: Ok, now I can click on someone else’s original post and then add a reply.  The problem has been fixed, but I still get the feeling I was doing something wrong the first time.

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